Molecular Biology


    Protocols in Current Issue
    Evaluation of the Sequence Variability within the PCR Primer/Probe Target Regions of the SARS-CoV-2 Genome
    Authors:  Kashif Aziz Khan and Peter Cheung, date: 12/20/2020, view: 680, Q&A: 0
    [Abstract] Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named 2019-nCoV) is responsible for the recent coronavirus disease (COVID-19) pandemic, and polymerase chain reaction (PCR) is the current standard method for diagnosis from patient samples. As PCR assays are prone to sequence mismatches due to mutations in the viral genome, it ...
    RNA ImmunoGenic Assay: A Method to Detect Immunogenicity of in vitro Transcribed mRNA in Human Whole Blood
    [Abstract] The mRNA therapeutics is a new class of medicine to treat many various diseases. However, in vitro transcribed (IVT) mRNA triggers immune responses due to recognition by human endosomal and cytoplasmic RNA sensors, but incorporation of modified nucleosides have been shown to reduce such responses. Therefore, an assay signifying important ...
    Charging State Analysis of Transfer RNA from an α-proteobacterium
    Authors:  Liang Yin and Caroline S. Harwood, date: 12/05/2020, view: 405, Q&A: 0
    [Abstract] Transfer RNA (tRNA) is an essential link between the genetic code and proteins. During the process of translation, tRNA is charged with its cognate amino acid and delivers it to the ribosome, thus serving as a substrate of protein synthesis. To analyze the charging state of a particular tRNA, total RNA is purified and analyzed on an acid-urea gel. ...
    Chromatin Immunoprecipitation (ChIP) to Assess Histone Marks in Auxin-treated Arabidopsis thaliana Inflorescence Tissue
    Authors:  André Kuhn and Lars Østergaard, date: 12/05/2020, view: 719, Q&A: 0
    [Abstract] Chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) or high-throughput sequencing (ChIP-seq) has become the gold standard for the identification of binding sites of DNA binding proteins and the localization of histone modification on a locus-specific or genome-wide scale, respectively. ChIP experiments can be divided into seven ...
    Agrobacterium-mediated Transformation of Sweet Basil (Ocimum basilicum)
    Authors:  Natasha Navet and Miaoying Tian, date: 11/20/2020, view: 944, Q&A: 1

    Sweet basil (Ocimum basilicum) is a popular herb with high economic value and is currently threatened by a severe oomycete disease. An efficient transformation method is a prerequisite for gene functional analysis to accelerate molecular breeding and deploy effective disease management strategies, and breeding through genetic engineering. Here we

    Reference-free Association Mapping from Sequencing Reads Using k-mers
    Authors:  Zakaria Mehrab, Jaiaid Mobin, Ibrahim Asadullah Tahmid, Lior Pachter and Atif Rahman, date: 11/05/2020, view: 711, Q&A: 0
    [Abstract] Association mapping is the process of linking phenotypes with genotypes. In genome wide association studies (GWAS), individuals are first genotyped using microarrays or by aligning sequenced reads to reference genomes. However, both these approaches rely on reference genomes which limits their application to organisms with no or incomplete ...
    Determination of Microtubule Lattice Parameters from Cryo-electron Microscope Images Using TubuleJ
    Authors:  Siou Ku, Cédric Messaoudi, Charlotte Guyomar, Charles Kervrann and Denis Chrétien, date: 11/05/2020, view: 560, Q&A: 0

    The α-β tubulin heterodimer undergoes subtle conformational changes during microtubule assembly. These can be modulated by external factors, whose effects on microtubule structure can be characterized on 2D views obtained by cryo-electron microscopy. Analysis of microtubule images is facilitated if they are straight enough to interpret

    Long-distance Transport in Bacterial Swarms Revealed by Single Nanoparticle Tracking
    Authors:  Jingjing Feng and Yan He, date: 11/05/2020, view: 453, Q&A: 0

    During swarming, high density flagella-driven bacteria migrate collectively in a swirling pattern on wet agar surfaces, immersed in a thin viscous fluid layer called “swarm fluid”. Though the fluid environment has essential role in the emergence of swarming behavior, the microscopic mechanisms of it in mediating the cooperation of

    DigiTAG–a RNA Sequencing Approach to Analyze Transcriptomes of Rare Cell Populations in Drosophila melanogaster
    Authors:  Lisa Landskron, Francois Bonnay, Thomas R. Burkard and Jürgen A. Knoblich, date: 11/05/2020, view: 735, Q&A: 0

    Cell-type specific transcriptional programs underlie the development and maintenance of organs. Not only distinct cell types within a tissue, even cells with supposedly identical cell fates show a high degree of transcriptional heterogeneity. Inevitable, low cell numbers are a major hurdle to study transcriptomes of pure cell populations. Here we

    Advances in Proximity Ligation in situ Hybridization (PLISH)
    Authors:  Monica Nagendran, Adam M Andruska, Pehr B Harbury and Tushar J Desai, date: 11/05/2020, view: 1013, Q&A: 0
    [Abstract] Understanding tissues in the context of development, maintenance and disease requires determining the molecular profiles of individual cells within their native in vivo spatial context. We developed a Proximity Ligation in situ Hybridization technology (PLISH) that enables quantitative measurement of single cell gene expression ...

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